metacoder 0.3.0

Bug fixes

• Fixed bug in calc_n_samples where the message reported the number of taxa instead of the number of rows in the table.
• Fixed bug in heat_tree_matrix that happened when factors were used for treatments (issue #240.
• zero_low_counts now ignores NAs instead of odd error.
• compare_groups now ignores NAs instaed of returning NaN

Improvements

• Added more_than option to calc_n_samples so that users can set the minimum threshold for whether a sample is counted or not instead of it always 1.
• Added calc_prop_samples function for calculating the proportion of samples with a value greater than 0 (issues #233.
• primersearch is faster and takes less memory by using ape::DNAbin objects internally.
• Made calc_taxon_abund about 5x faster.

New features

• taxmap objects can be converted to phyloseq objects using as_phyloseq.
• Added parser for uBiome data.

Changes

• primersearch now takes and returns a taxmap object with results added as tables. primersearch_raw is a new function that behaves like the old primersearch did, returning a table.
• The dataset option of many functions has been renamed to data to match the option name in the taxa package.
• Numerous spelling fixes.